[gmx-users] charge group moved too far between two domain decomposition steps?

[Mark Abraham]

Hi,

You should start by using a time step more appropriate to your use of
constraints = none, or vice versa.

Mark

On Wed, Oct 22, 2014 at 4:26 AM, Kester Wong <Kester2014 at ibs.re.kr> wrote:

> Dear all,
>
>
> I am intrigued by the error that I have received this morning, as follows:
>
>
>
> The charge group starting at atom 37920 moved more than the distance
> allowed by the domain decomposition (1.400000) in direction Y
>
> distance out of cell 7.144197
>
> Old coordinates:   54.499   39.697   14.058
>
> New coordinates:   54.499   39.697   14.058
>
> Old cell boundaries in direction Y:   19.468   32.846
>
> New cell boundaries in direction Y:   18.667   32.553
>
>
> If the charge group moved, if any, then shouldn't the new coordinates be
> showing different values?
>
> It was a new NPT calculation that I continued from a 20ns NVT run, so it
> should be equilibrated well enough, for a simple water on graphene system.
>
>
> Using GROMACS 5.0, I was unable to start the NPT with Berendsen
> thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my
> tau-T was 0.5, following the general rule of thumb, that tau-P should be
> larger than tau-T to allow thermal degrees of freedom to equilibrate faster
> than the box size).
>
>
> Should I reduce tau-P?
>
>
>
>
> Below is my NPT.mdp parameters:
>
> ; RUN CONTROL PARAMETERS
>
> integrator               = md
>
> tinit                    = 20000.000
>
> dt                       = 0.002    ;  2 fs
>
> nsteps                   = 5000000  ; 10,000 ps
>
> comm-mode                = Linear
>
> nstcomm                  = 10
>
>
> emtol                    = 0.001
>
> niter                    = 30
>
>
> ; OUTPUT CONTROL OPTIONS
>
> nstxout                  = 5000    ; save coordinates every 8 ps
>
> nstvout                  = 5000    ; save velocities every 8 ps
>
> nstfout                  = 0
>
> nstlog                   = 5000    ; update log file every 8 ps
>
> nstenergy                = 5000    ; save energies every 8 ps
>
> ;nstxtcout is replaced with nstxout-compressed
>
> nstxout-compressed       = 5000    ; no. of steps between writing
> coordinates using lossy compression
>
> ;xtc-precision is replaced with compressed-x-precision
>
> compressed-x-precision   = 3000    ; precision with which to write to the
> compressed trajectory file
>
>
> ; Periodic boundary conditions: xyz (default), no (vacuum)
>
> cutoff-scheme            = Verlet ; default for GROMACS-5.0
>
> nstlist                  = 1      ; A smaller nstlist may reduce LINCS
> warnings
>
> ns-type                  = grid   ;
>
> pbc                      = xyz
>
> ;periodic_molecules       = yes  ; cannot be used with SHAKE
>
> ; nblist cut-off
>
> rlist                    = 1.40   ; short-range neighbourlist cutoff
>
> nstcalclr                = 1
>
>
> coulombtype              = PME
>
> coulomb-modifier         = Potential-shift-Verlet
>
> r_coulomb                = 1.40  ; short-range electrostatic cutoff
>
> rcoulomb-switch          = 0     ; used when potential-switch
> (coulomb-modifier) is specified
>
> epsilon-r                = 1     ; default value=1
>
> pme_order                = 4
>
> fourierspacing           = 0.12
>
> fourier_nx               = 0
>
> fourier_ny               = 0
>
> fourier_nz               = 0
>
> ewald_rtol               = 1e-05
>
> ewald_geometry           = 3d
>
> epsilon_surface          = 0      ; Use 0 when simulation is done with PME
>
>
>
> ;vdw-type = switch is replaced with the following two flags in GROMACS-5.0
>
> vdwtype                  = Cut-off
>
> vdw_modifier             = Potential-switch
>
> ; cut-off lengths
>
> rvdw-switch              = 1.00
> rvdw                     = 1.40   ; short-range van der Waals cutoff
>
> constraints              = none
> constraint-algorithm     = SHAKE
> continuation             = yes    ; starting from NVT run
> Shake-SOR                = no
> shake-tol                = 0.0001
> ;lincs-order              = 4     ; accuracy of LINCS
> ;lincs-iter               = 24    ; also related to accuracy
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> ;lincs-warnangle          = 30
>
> Tcoupl                   = v-rescale
> nh-chain-length          = 1    ; the leapfrog md integrator only supports
> 1
> ; Groups to couple separately
> tc-grps                  = GRA SOL
> ; Time constant (ps) and reference temperature (K)
> tau-t                    = 0.5 0.5
> ref-t                    = 300 300
> nsttcouple               = 20  ; added by k-wong ; not specified in
> Yanbin's MDP
>
> Pcoupl                   = Parrinello-Rahman
> Pcoupltype               = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p                    = 5.0  ; time constant in ps
> compressibility          = 4.5e-5  ; isothermal compressibility of water,
> bar^-1
> ref-p                    = 1.0  ; reference pressure, in bar
>
>
> ; Non-equilibrium MD stuff
> freezegrps               = GRA
> freezedim                = Y Y Y
>
> gen_vel                  = no
> ;gen_temp                 = 300
> ;gen_seed                 = 173529
>
>
> Thanks in advance!
>
>
>
> Regards,
>
> Kester
>
>
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